Their headteacher said that, as the filming was done in school time, it counted as work experience.
The school received a £1,370 donation from film-makers Warner Bros for the pupils' efforts.
The kids were allowed to keep the cash they earned at weekends.
However, extras from another school in the area were allowed to keep their weekday earnings too.
The local council said that the schools had "different policies".
"Lochaber have dealt with Warner Bros a lot and have developed a policy where they make a donation to the school fund," the council spokesman added.
Harry Potter And The Prisoner Of Azkaban will see Daniel Radcliffe, Rupert Grint and Emma Watson returning to their roles as Harry, Ron and Hermione.
It will be the third film about the boy wizard.